How to run prepDE.py3?

Question

[SH]

Hello,

• I ran stringtie and obtained merge.gtf as a result. Now, I want to run prepDE.py3 to obtain gene.csv and transcript.csv. I thought prepDE.py3 was a function that was embedded together with stringtie when I installed it.
• However, when I type "./prepDE.py3" or "prepDE.py3" in the Ubuntu terminal, it shows an error message "command not found".
• Currently, "sudo apt-get install python3-pip" has been completed. After that, I tried "sudo pip3 install prepDE.py3", but it shows an error message "ERROR: Could not find a version that satisfies the requirement prepDE.py3 (from versions: none) ERROR: No matching distribution found for prepDE.py3".
• So, I downloaded prepDE.py3 in the working folder by executing "wget https://github.com/gpertea/stringtie/raw/master/prepDE.py3". In conclusion, I want to run prepDE.py3 in the Ubuntu terminal. How can I do it?

Thank you in advance for your help.

Answer 1

[Barry Digby]

The shebang in prepDE.py3 looks for the first version of python3 installed in your path (#!/usr/bin/env python3) so if you have python3, just type python prepDE.py3 :)

If your base python is 2.7 install python3.* in an environment using conda